Non-Coding DNA/Introns

Bad name and may die out as we find out what these actually do!!

In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs), while others are not transcribed or give rise to RNA transcripts of unknown function. The amount of noncoding DNA varies greatly among species. For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.  Introns are also really included as Non-coding DNA. But they are not Spacers (see below)

Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as "junk DNA", particularly in the lay press. However, it has been known for decades that many noncoding sequences are functional. These include genes for functional RNA molecules (see above) and sequences such as origins of replication, centromeres, and telomeres.

Examples of noncoding RNA include ribosomal RNA, transfer RNA, Piwi-interacting RNA (PiRNA)  and microRNA.

Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, particularly those in spermatogenesis. They are distinct from microRNA (miRNA) in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity.

In the human genome, over 98% of DNA is classified as noncoding DNA and can be transcribed to regulatory noncoding RNAs (i.e. tRNAs, rRNAs), origins of DNA replication, centromeres, telomeres and scaffold attachment regions (SARs).

Noncoding regions are most commonly referred to as 'junk DNA', however, this term is misleading as noncoding DNA does have functional importance.

The proportion of coding and noncoding DNA within organisms varies and the amount of noncoding DNA typically correlates with organism complexity, though there are many notable exceptions.

noncoding

DNA which does not code for protein

intron

a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded

intergenic

describing the noncoding sections of nucleic acid between genes, this is the majority of non-coding DNA actually.  This is Spacer DNA

Spacer DNA or intergenic spacer (IGS) is a region of non-coding DNA between genes. The term is used particularly for the spacer DNA between the many tandemly repeated copies of the ribosomal RNA genes.

In bacteria, spacer DNA sequences are only a few nucleotides long. In eukaryotes, they can be extensive and include repetitive DNA, comprising the majority of the DNA of the genome.[3] In ribosomal DNA, there are spacers within and between gene clusters, called internal transcribed spacer (ITS) and external transcribed spacers (ETS), respectively. In animal, the mitochondrial DNA genes generally have very short spacers. In fungi, mitochondrial DNA spacers are common and variable in length, and they may also be mobile.

Since spacer DNA sequence changes much more rapidly in evolution than the gene sequence, it is thought that spacer DNA does not have a function that depends on its sequence, although it may have sequence-independent function.

Biologists have discovered the linchpin to what they’re calling the “big bang” of immune cell development: the previously overlooked “non-coding” regions of DNAbetween genes.  SEpt 2017 Univ of California-San Diego. See "Overlooked oppposite. They found that these regions of DNA activate a change in DNA’s 3D structure that unites promoters and enhancers with a high degree of accuracy. The process they observed in mice allowed T cells to develop properly. These cells are the building blocks of the immune system, which is why problems with their development can cause diseases such as leukemia and lymphoma.

All cells have ribosomes, molecular machines that build proteins. Ribosome assembly is sensitive to stresses like desiccation. So we asked if the many introns found in ribosomal DNA (rDNA) of lichen fungi affect their remarkable desiccation tolerance. Using CRISPR, we moved introns from a lichen fungus into the rDNA of yeast, a fungus with no rDNA introns. Yeast desiccation tolerance went up 1000-fold with introns. We think that introns are not causing the resistance directly, but their removal during ribosome assembly slows it down, which then causes activation of genes protecting the cell from desiccation damage. In the presence of rDNA introns such genes remain on, maintaining cells on constant alert even in absence of desiccation.   New experiment JAn 2019 Duke University.

See article June 2020 "essential role in rice...." opposite    "This study shows that non-coding RNAs, derived from regions of the genome that were thought to be non-functional, are vital for plant reproduction. Exploring non-coding RNAs further is an exciting and important area of research."

Non-Coding DNA/Introns

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